+Open data
-Basic information
Entry | Database: PDB / ID: 5l9f | ||||||
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Title | S. enterica HisA mutant - D10G, G11D, dup13-15, G44E, G102A | ||||||
Components | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase | ||||||
Keywords | ISOMERASE / HisA / protein evolution / IAD model / TrpF | ||||||
Function / homology | Function and homology information 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella choleraesuis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å | ||||||
Authors | Guo, X. / Soderholm, A. / Selmer, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes. Authors: Newton, M.S. / Guo, X. / Soderholm, A. / Nasvall, J. / Lundstrom, P. / Andersson, D.I. / Selmer, M. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9f.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9f.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 5l9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9f ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9f | HTTPS FTP |
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-Related structure data
Related structure data | 5ab3C 5ac7C 5ac8C 5g1tSC 5g1yC 5g2hC 5g2iC 5g2wC 5g4eC 5g4wC 5g5iC 5l6uC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27649.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: hisA, AL032_11160, IN36_13675, IN69_03475, IN95_11755 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0M0QTF7, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M lithium sulfate, 0.1 M sodium acetate pH4.5, 30 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. all: 82382 / Num. obs: 17013 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.988 / Rsym value: 0.204 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.795 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5g1t Resolution: 2.594→49.48 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.594→49.48 Å
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Refine LS restraints |
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LS refinement shell |
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